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Juan Fernández and Desventuradas are two oceanic archipelagos located in the southeastern Pacific Ocean far off the Chilean coast that received protected status as marine parks in 2016. Remoteness and access difficulty contributed to historically poor biodiversity sampling and limited associated research. This is particularly noticeable for bivalves, with most prior regional publications focused on single taxa or un-illustrated checklists. This study investigates marine bivalves collected between the intertidal and 415 m depth during (1) the 1997 IOC97 expedition aboard the M/V Carlos Porter, with special focus on scuba-collected micro-mollusks of both archipelagos, (2) two expeditions by the R/V Anton Bruun (Cruise 12/1965 and Cruise 17/1966), and (3) Cruise 21 of USNS Eltanin under the United States Antarctic Program, which sampled at Juan Fernández in 1965. Also, relevant historical material of the British H.M.S. Challenger Expedition (1873-1876), the Swedish Pacific Expedition (1916-1917), and by German zoologist Ludwig H. Plate (1893-1895) is critically revised. A total of 48 species are recognized and illustrated, including 19 new species (described herein) and six other potentially new species. The presence of two species mentioned in the literature for the region (Aulacomya atra and Saccella cuneata) could not be confirmed. The genera Verticipronus and Halonympha are reported for the first time from the Eastern Pacific, as are Anadara and Condylocardia from Chilean waters. Lectotypes are designated for Arca (Barbatia) platei and Mytilus algosus. These findings double the number of extant bivalve species known from the Juan Fernández and Desventuradas archipelagos, highlighting the lack of attention these islands groups have received in the past. A high percentage of species endemic to one or both archipelagos are recognized herein, accounting for almost 78% of the total. The newly recognized level of bivalve endemism supports the consideration of Juan Fernández and Desventuradas as two different biogeographic units (Provinces or Ecoregions) of the Eastern Pacific Ocean.

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Introduction: Sporotrichosis is a subcutaneous mycosis caused by fungi of the genus Sporothrix sp. Phenotypic and genotypic differences have been associated with their geographic distribution, virulence, or clinical manifestation of sporotrichosis. In the past decade, the interest in identifying species of the Sporothrix sp. has been increasing, due to its epidemiological importance and, in consequence, is important to know how to preserve them for future studies, in culture collection. Aims: The purposes of this study were to analyze the global distribution of environmental isolates and/or causal agents of sporotrichosis identified by polyphasic taxonomy, with mandatory use of molecular identification, and to evaluate the percentages and distribution of isolates stored in culture collections. Methods: A systematic review of articles on animal and human sporotrichosis and/or environmental isolation of the fungus, from 2007 to 2023, was done. Results: Our results demonstrated that, S. globosa, S. schenckii, and S. brasiliensis were the most identified species. With respect to the deposit and maintenance of species, we observed that only 17% of the strains of Sporothrix sp. isolated in the world are preserved in a culture collection. Conclusions: This systematic review confirmed a difficulty in obtaining the frequency of Sporothrix species stored in culture collection and insufficient data on the molecular identification mainly of animal sporotrichosis and isolation of Sporothrix sp. in environmental samples.

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Currently, according to the most recent Simuliidae World Inventory, there are 97 valid species of blackflies recorded in Brazil, some of which act as vectors for zoonoses such as human onchocerciasis and mansonellosis in the northern and central-western regions of the country. Meanwhile, other species can cause serious socioeconomic problems due to the nuisance of female bites. Therefore, accurate knowledge of their distribution is crucial for the development and implementation of successful preventive strategies. With this aim, this study reviewed and updated the geographical distribution of the blackfly fauna throughout the Brazilian states. The data were compiled from three main sources: geographic information of material deposited at the Simuliidae Collection of the Instituto Oswaldo Cruz (CSIOC-IOC), a comprehensive review of scientific literature, and online biodiversity databases. We present a total of 71 new distribution records of 38 different Simuliidae species for 24 Brazilian states. Neither of these sets of records has been included in the Simuliidae World Inventory. Consequently, an updated Brazilian Simuliidae checklist, comprising a total of 98 valid species, is presented, highlighting these new distribution records. We also discuss six dubious records for the country and the implications of this updated data for the Simuliidae species richness of Brazil, its states, and biomes. This information is essential for future studies in the taxonomy, systematics, and biogeography of this family in Brazil.

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Yersinia pestis, the causative agent of plague, is a highly virulent bacterium that poses a significant threat to human health. Preserving this bacterium in a viable state is crucial for research and diagnostic purposes. This paper presents and evaluates a simple lyophilization protocol for the long-term storage of Y. pestis strains from Fiocruz-CYP, aiming to explore its impact on viability and long-term stability, while replacing the currently used methodologies. The lyophilization tests were conducted using the non-virulent Y. pestis strain EV76, subjected to the lyophilization process under vacuum conditions. Viability assessment was performed to evaluate the effects of lyophilization and storage conditions on Y. pestis under multiple temperature conditions (- 80 °C, - 20 °C, 4-8 °C and room temperature). The lyophilization protocol employed in this study consistently demonstrated its efficacy in maintaining high viability rates for Y. pestis samples in a up to one year follow-up. The storage temperature that consistently exhibited the highest recovery rates was - 80 °C, followed by - 20 °C and 4-8 °C. Microscopic analysis of the post-lyophilized cultures revealed preserved morphological features, consistent with viable bacteria. The high viability rates observed in the preserved samples indicate the successful preservation of Y. pestis using this protocol. Overall, the presented lyophilization protocol provides a valuable tool for the long-term storage of Y. pestis, offering stability, viability, and functionality. By refining the currently used methods of lyophilization, this protocol can improve long-term preservation for Y. pestis strains collections, facilitating research efforts, diagnostic procedures, and the development of preventive and therapeutic strategies against plague.

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Abstract Introduction: Molecular divergence thresholds have been proposed to distinguish recently separated evolutive units, often displaying more accurate putative species assignments in taxonomic research compared to traditional morphological approaches. This makes DNA barcoding an attractive identification tool for a variety of marine invertebrates, especially for cryptic species complexes. Although GenBank and the Barcode of Life Data System (BOLD) are the major sequence repositories worldwide, very few have tested their performance in the identification of echinoderm sequences. Objective: We use COI echinoderm sequences from local samples and the molecular identification platforms from GenBank and BOLD, in order to test their accuracy and reliability in the DNA barcoding identification for Central American shallow water echinoderms, at genus and species level. Methods: We conducted sampling, tissue extraction, COI amplification, sequencing, and taxonomic identification for 475 specimens. The 348 obtained sequences were individually enquired with BLAST in GenBank as well as using the Identification System (IDS) in BOLD. Query sequences were classified depending on the best match result. McNemar's chi-squared, Kruskal-Wallis's and Mann-Whitney's U tests were performed to prove differences between the results from both databases. Additionally, we recorded an updated list of species reported for the shallow waters of the Central American Pacific. Results: We found 324 echinoderm species reported for Central American Pacific shallow waters. Only 118 and 110 were present in GenBank and BOLD databases respectively. We proposed 325 solved morphology-based identities and 21 provisional identifications in 50 putative taxa. GenBank retrieved 348 molecular-based identifications in 58 species, including twelve provisional identifications in tree taxa. BOLD recovered 170 COI identifications in 23 species with one provisional identification. Nevertheless, 178 sequences retrieved unmatched terms (in 34 morphology-based taxa). Only 86 sequences (25 %) were retrieved as correct identifications and 128 (37 %) as identification errors in both platforms. We include 84 sequences for eleven species not represented in GenBank and 65 sequences for ten species in BOLD Echinoderm COI databases. The identification accuracy using BLAST (175 correct and 152 incorrect identifications) was greater than with IDS engine (110 correct and 218 identification errors), therefore GenBank outperforms BOLD (Kruskal-Wallis = 41.625, df = 1, p < 0.001). Conclusions: Additional echinoderm sample references are needed to improve the utility of the evaluated DNA barcoding identification tools. Identification discordances in both databases may obey specific parameters used in each search algorithm engine and the available sequences. We recommend the use of barcoding as a complementary identification source for Central American Pacific shallow water echinoderm species.

Resumen Introducción: Se han propuesto los umbrales de divergencia molecular para distinguir unidades evolutivas recientemente separadas, que a menudo muestran asignaciones de especies putativas más precisas en la investigación taxonómica en comparación con los enfoques morfológicos tradicionales. Esto hace que los Códigos de Barras de ADN sean una herramienta de identificación atractiva para una variedad de invertebrados marinos, especialmente para complejos de especies crípticas. Aunque GenBank y Barcode of Life Data System (BOLD) son los principales repositorios de secuencias en todo el mundo, muy pocos han probado su desempeño en la identificación de secuencias de equinodermos. Objetivo: Utilizamos secuencias de equinodermos COI de muestras locales y las plataformas de identificación molecular de GenBank y BOLD, para probar su precisión y confiabilidad en la implementación de códigos de barras de ADN para equinodermos de aguas someras de Centroamérica, a nivel de género y especie. Métodos: Realizamos muestreo, extracción de tejido, amplificación de COI, secuenciación e identificación taxonómica de 475 especímenes. Las 348 secuencias obtenidas fueron consultadas individualmente con BLAST en GenBank así como utilizando el Sistema de Identificación (IDS) en BOLD. Las secuencias consultadas se clasificaron según el mejor resultado de coincidencia. Se realizaron las pruebas chi-cuadrado de McNemar, Kruskal-Wallis y U de Mann-Whitney para comprobar diferencias entre los resultados de ambas bases de datos. Además, registramos una lista actualizada de especies reportadas para las aguas someras del Pacífico Centroamericano. Resultados: Encontramos 324 especies de equinodermos reportadas para aguas someras (< 200 m) del Pacífico centroamericano. Sólo 118 y 110 estaban presentes en las bases de datos GenBank y BOLD respectivamente. Propusimos 325 identidades resueltas basadas en morfología y 21 identificaciones provisionales en 50 taxones putativos. GenBank recuperó 348 identificaciones de base molecular en 58 especies, incluidas doce identificaciones provisionales en tres taxones. BOLD recuperó 170 identificaciones de COI en 23 especies con una identificación provisional. Sin embargo, 178 secuencias recuperaron términos no coincidentes (en 34 taxones basados en morfología). Sólo 86 secuencias (25 %) se recuperaron como identificaciones correctas y 128 (37 %) como errores de identificación en ambas plataformas. Incluimos 84 secuencias para once especies no representadas en GenBank y 65 secuencias para diez especies ausentes en las bases de datos BOLD Echinoderm COI. La precisión de la identificación usando BLAST (175 identificaciones correctas y 152 incorrectas) fue mayor que con el motor IDS (110 correctas y 218 errores de identificación), por lo tanto, GenBank supera a BOLD (Kruskal-Wallis = 41.625, df = 1, p < 0.001). Conclusiones: Se necesitan muestras adicionales de equinodermos de referencia para mejorar la utilidad de las herramientas de identificación de códigos de barras de ADN evaluadas. Las discordancias de identificación en ambas bases de datos pueden obedecer a parámetros específicos utilizados en cada algoritmo de búsqueda y a las secuencias disponibles. Recomendamos el uso de códigos de barras como fuente de identificación complementaria para las especies de equinodermos de aguas someras del Pacífico centroamericano.

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Resumen Introducción: Las especies de las clases Crinoidea y Asteroidea se distribuyen en gran variedad de hábitats en todos los océanos desde la zona intermareal hasta grandes profundidades, existen pocos registros en aguas mexicanas, a profundidades superiores a los 200 m, los escasos registros existentes datan de documentos históricos de la literatura especializada y los ejemplares se resguardan en colecciones científicas extranjeras. Objetivo: Contribuir a la recopilación de información de los ejemplares resguardados en la Colección Nacional de Equinodermos (CNE) del Instituto de Ciencias del Mar y Limnología (ICML), UNAM y proveer un inventario de las especies de crinoideos y asteroideos que habitan en zonas profundas del talud de la Península de Yucatán, México. Métodos: Del año 2005 al 2014 se recolectaron ejemplares de crinoideos y asteriodeos en cuatro cruceros en el B/O "Justo Sierra" BIOREPES 1 y 2 y COBERPES 2 y 6. Se realizaron arrastres con red camaronera en 80 estaciones de muestreo. Resultados: El listado taxonómico comprende 1146 ejemplares, de los cuales 204 son crinoideos del orden Comatulida, distribuidos en tres familias tres géneros y tres especies y 942 asteroideos distribuidos en seis órdenes, 11 familias, 21 géneros y 28 especies. Se obtuvieron los registros nuevos para la CNE: Democrinus rawsonii y Atelecrinus balanoides en crinoideos. Astropecten alligator, Hymenaster modestus, Calyptraster personatus, Pteraster militarioides militarioides, Sclerasterias contorta en asteroideos. Con esta información se incrementan los registros de crinoideos y asteroideos (de profundidad mayor a 200 m) para los estados de Yucatán (16) y Quintana Roo (16).

Abstract Introduction: The species of the Crinoidea and Asteroidea classes are distributed in a wide variety of habitats in all oceans from the intertidal zone to great depths, there are few Mexican records in depths greater than 200 m, the few existing records date from historical documents in the specialized literature and the specimens are kept in foreign scientific collections. Objective: Contribute to the collection of information on the specimens kept in the Colección Nacional de Equinodermos (CNE) of Instituto de Ciencias del Mar y Limnología (ICML), UNAM and provide an inventory of the species of crinoids and asteroids that inhabit deep areas of the slope of the Yucatan Peninsula, Mexico. Methods: From 2005 to 2014, specimens of crinoids and asterioids were collected through four cruises in the B/O "Justo Sierra" BIOREPES 1 and 2 and COBERPES 2 and 6, shrimp net trawls were carried out at 80 sampling stations. Results: The taxonomic list includes 1146 specimens, of which 204 crinoids are of the order Comatulida, distributed in three families, three genera and three species and 942 asteroids distributed in six orders, 11 families, 21 genera and 28 species. New records were obtained for CNE: Democrinus rawsonii and Atelecrinus balanoides in crinoids. Astropecten alligator, Hymenaster modestus, Calyptraster personatus, Pteraster militarioides militarioides, Sclerasterias contorta in asteroids. With this information, the records of crinoids and asteroids (deeper than 200 m) increase for the states of Yucatan (16) and Quintana Roo (16).

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Background: The digital inventory of paleontological material stored in Chilean museums is highly relevant as it increases accessibility to information, both locally and over long distances, while reducing wear and tear on specimens caused by physical manipulation. The Fossil Collection database of the Museum of Zoology of the University of Concepción (UCC_MZUC_FOS) includes 144 records, with the main representatives being marine invertebrates of the Bivalvia, Echinoidea and Gastropoda classes. Notable species include Encopecalderensis, Hemiasterwayensis, Zygochlamyspatagonica and Retrotapesexalbidus, most of which come from important Chilean fossil sites. Material was collected between 1970 and 2017, with a large portion of it being donated and identified by Professor Emeritus Hugo I. Moyano and Dr. Alberto Larraín. Although the specimens contained in the resource offer basic collecting information, they substantially contribute to sharing knowledge on the fossils kept in the museums throughout the country, while providing data on their distribution. New information: This resource corresponds to the first publication of data on faunal fossils from a museum collection in Chile on the Global Biodiversity Information Facility (GBIF) platform, thereby enhancing the understanding and documentation of Chile's paleontological heritage and its national biodiversity.

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Per- and polyfluoroalkyl substances (PFAS) in the environment pose persistent and complex threats to human and wildlife health. Around the world, PFAS point sources such as military bases expose thousands of populations of wildlife and game species, with potentially far-reaching implications for population and ecosystem health. But few studies shed light on the extent to which PFAS permeate food webs, particularly ecologically and taxonomically diverse communities of primary and secondary consumers. Here we conducted >2000 assays to measure tissue-concentrations of 17 PFAS in 23 species of mammals and migratory birds at Holloman Air Force Base (AFB), New Mexico, USA, where wastewater catchment lakes form biodiverse oases. PFAS concentrations were among the highest reported in animal tissues, and high levels have persisted for at least three decades. Twenty of 23 species sampled at Holloman AFB were heavily contaminated, representing middle trophic levels and wetland to desert microhabitats, implicating pathways for PFAS uptake: ingestion of surface water, sediments, and soil; foraging on aquatic invertebrates and plants; and preying upon birds or mammals. The hazardous long carbon-chain form, perfluorooctanosulfonic acid (PFOS), was most abundant, with liver concentrations averaging >10,000 ng/g wet weight (ww) in birds and mammals, respectively, and reaching as high 97,000 ng/g ww in a 1994 specimen. Perfluorohexanesulfonic acid (PFHxS) averaged thousands of ng/g ww in the livers of aquatic birds and littoral-zone house mice, but one order of magnitude lower in the livers of upland desert rodent species. Piscivores and upland desert songbirds were relatively uncontaminated. At control sites, PFAS levels were strikingly lower on average and different in composition. In sum, legacy PFAS at this desert oasis have permeated local aquatic and terrestrial food webs across decades, severely contaminating populations of resident and migrant animals, and exposing people via game meat consumption and outdoor recreation.

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A dataset about three topics is provided, as a follow-up to the article "Mexico's forest diversity: common tree species and proposed forest-vegetation provinces" by Ricker et al. [1]. Firstly, 6927 site locations are provided for 22,532 trees of 1452 species. Secondly, measurements of basic wood-densities are reported for 779 tree species, obtained from 5256 trunk-core samples from Mexico's national forest inventory, and ranging from 0.05 to 0.93 g/cm3. Third, the data and maps of the forest-vegetation provinces from [1] were updated with the new cartography of Mexico's vegetation and land use (base year 2018). The maps are available now in an adjusted presentation as a shapefile-set for ArcGIS, as well as map-package and image files.

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SUMMARY OBJECTIVE: The aim of this study was to assess the results and efficiency of two real-time polymerase chain reaction procedures for detecting human papillomavirus utilizing urine samples. METHODS: This study comprised 151 patients who had previously tested positive for human papillomavirus in their cervical samples. Two different commercial real-time polymerase chain reaction techniques were used for identification and genotyping human papillomavirus in urine specimens. The urine samples of 151 patients were evaluated via the Roche Cobas test, and the urine samples of 91 patients were also evaluated via the Qiagen test. RESULTS: The overall consistency of urine and cervical swab specimens for the identification of human papillomavirus in Roche Cobas and Qiagen tests were 44.8 and 44%, respectively. The rates of positive human papillomavirus results from urine samples were 57 and 70.3%, respectively. The overall concordance among Roche Cobas and Qiagen tests utilizing urine samples for human papillomavirus type 16/18 was 84.3% with a kappa value of 0.675, and for other high-risk-human papillomavirus, it was 75.60% with a kappa value of 0.535. Roche Cobas showed high concordance with Qiagen test. CONCLUSION: human papillomavirus positivity was not detected in all urine samples. It is still inappropriate to recommend the use of urine liquid biopsy for the accurate and reliable detection of human papillomavirus. Due to the lack of a standardized tool, the utilization of urine samples as a screening human papillomavirus test remains a challenge.